Do the tactical ones count? FFT had some very good mechanics, including CT (essentially a proper way to work speed into turn order along with getting faster turns by not moving, not attacking, or both) increased damage vs charging enemies, good ol' flanking and height advantages (which even a lot of western tactical games don't bother with, having entirely flat terrain) and while silly, the zodiac alignment thing added another layer to things as well. Along with just a ton of cool individual ability mechanics like stealing, jumping, various status effects, geomancy, various reaction skills and movement abilities, being able to ride chocobos, dismount, and have them attack on their own... plenty of cool shit. The Faith/Brave mechanics were cool too, though abusing them led to some very OP shit.
Vanguard Bandits had some interesting rock/paper/scissors combat as well, with dodge vs counter vs defending various types of attacks, and a fatigue mechanic, so even weaker units could take on a powerful enemy by whaling on him till he's too exhausted to defend himself.
Brigandine is mostly bog standard combat mechanics as far as what abilities do and how damage is calculated and such, but the rune area each commander needed to keep monsters in was a nice touch, as was the option of taking down a commander to make his bodyguards disappear (doubly so vs a faction leader.)
FF10 actually had a good turn order system, with different abilities taking different amounts of time and fast characters getting multiple turns vs slow ones. The way stats scaled was interesting as well, I can't recall if it was quadratic or exponential but the difference between 50 str and 30 str was WAAAY more than 40% more damage, and a ~10 point difference between accuracy and evasion stats meant you were hitting air almost always.
The rage mechanic introduced in lufia 2 and copied by the FF series is a good one too. Was especially good in lufia 2 since you could customize what you used it for with equipment, making gear not just a matter of best stats in slot.
Ogre Battle's system of units getting multiple turns in each 'round' of combat and the potential to win without killing your opponent (or lose without dying) was interesting as well. Excellent campaign and character growth mechanics too.
Breath of Fire series has had some interesting mechanics over the years as well. 3 had a very cool dragon system that essentially let you make a custom character on the fly in combat ranging from glass cannons to tanks that replaced your party and a bunch of weird niche cases, assuming you had the right genes available. Pity you spend much of the game without much selection and they weren't balanced all that well, or needed since most fights were too easy. BoF 5: DQ is more noteworthy for it's out of combat mechanics I suppose, it certainly had unique combat but I found it pretty tedious for the most part.
Front Mission series (I really only played 3) with it's locational damage and pilot ejection (and mech capture!) mechanics was really cool as well. Actually the combat skills were pretty cool too. Watching your ace melee pilot walk up and just unload on some poor fuck with half a dozen swings (essentially a high tiered crit since multiple skills proccing gave multiple attacks, and was quite rare) always felt amazing. And the different weapon types all felt pretty unique due to the variations in range, the way they tended to deal locational damage, their elements, etc.
Star Ocean 2 had some cool combat mechanics in regards to different types of knockback, float (vertical juggling, basically), stun, blocking, etc. mechanics and varied enemy types. A heavy knight with a shield might need to be struck from behind (or with magic) while a lighter mage can be hit head on. But while you might one shot that mage, something like a ninja or berserker might get knocked back really far by certain attacks and thereby escape being caught in a combo, so you'd want to use attacks that knock them up rather than back, unless you wanted to keep them at a distance, in which case you could use the knockback defensively. All that kinda stuff along with the various randomly activating battle skills made things a lot more dynamic than you'd expect. Although the difficulty was lacking by default and on higher settings it turned into 'How do I cheese this game?'
Earthbound's rolling HP meter (essentially it took some real world time before a big hit would finish dealing the damage as the numbers ticked down, giving you a chance to heal or land a last desperate attack) was a neat quirk and much better implementation of adding real time to make combat intense than shit like timed hits or the botched ATB system present in CT and FF4-9.
Phantasy Star's system of techniques (which use a pool of generic points) vs skills (which can be used a specific number of times each individually before resting, so you might have an uber heal you can use once before resting regardless of everything else) was pretty cool, along with a cool combo system pretty similar to chrono trigger's.
SaGa Frontier has some really cool combat mechanics, including the HP/LP/WP/JP system (basically two different health pools and two different 'magic' pools) learn new special attacks (or immunities to certain attacks!) during battle, especially in desperate situations, and a rather unique take on the combo system that has combos occur dynamically based on attack traits rather than a bunch of pre scripted ones. Character growth and the different races was really cool as well, along with some really cool spell effects like glass shield, overdrive, stasis, light sword, and a bunch of other cool shit.
Plenty of jrpgs have interesting mechanics, they're just wasted because they didn't bother to tune the difficulty so they matter. Pretty much all these games have some pretty simple strategies that, while perhaps not optimal, are good enough to handle all threats in a repetitive way.
